The CSS style part which loads the language flags doesn't appear on the source code of your site.

It can be because of:

1. You have modified modules/mod_gtranslate/tmpl/default.php or any other file in mod_gtranslate folder2. You have a template override set in your templates/current_template/html/mod_gtranslate3. You have placed the language selector code directly into your template page without the stylesheet4. There is some plugin installed on your site which removes the <style> definition from your source code

This is not connected with the Pro version. If you were able to see the flags before, just remember what you have done on your site after which they disappeared.